SMTL ID : 7ytj.1

Cryo-EM structure of VTC complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-1-mer

Ligands

3 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 9 residues within 4Å: Chain A: K.3, F.4, Y.23, K.27, K.130, K.133, K.134, K.137 Chain E: R.255 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:F.4, A:Y.23, A:Y.23 Salt bridges: A:K.27, A:K.27, A:K.130, A:K.130, A:K.130, A:K.133, A:K.133, A:K.134, A:K.134, A:K.137, A:K.137, A:K.138, E:R.255 IHP.2: 11 residues within 4Å: Chain A: T.199, K.201, R.254, E.280, K.282, S.293, K.295, R.362, N.427, K.429, K.459 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Y.242, A:Y.242, A:S.293, A:S.293, A:N.427 Salt bridges: A:K.201, A:K.201, A:R.254, A:K.282, A:K.282, A:K.282, A:K.295, A:K.295, A:K.295, A:R.362, A:K.429, A:K.429, A:K.459 IHP.4: 7 residues within 4Å: Chain A: K.301, R.303, K.321 Chain E: K.391, K.393, Y.409, Q.413 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain E Salt bridges: A:R.303, A:K.321, A:K.321, A:K.321, E:K.391, E:K.391, E:K.391, E:K.393 Hydrogen bonds: E:Y.409, E:Q.413

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.3: 17 residues within 4Å: Chain A: L.641, G.644, T.648, Y.652 Chain B: V.42, M.43, G.46, G.50, F.54 Chain D: F.54 Chain E: L.745, L.749, S.752, I.753, S.756, E.761 Ligands: PC1.7 11 PLIP interactions: 5 interactions with chain E, 3 interactions with chain A, 2 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: E:L.745, E:L.749, E:L.749, E:I.753, A:L.641, A:Y.652, A:Y.652, D:F.54, D:F.54, B:F.54 Hydrogen bonds: E:S.756 PC1.7: 25 residues within 4Å: Chain B: M.43 Chain C: T.41, G.45, G.46, L.47, V.49, G.50, L.51, F.54, M.71 Chain D: M.43, L.44, G.46, L.47, L.51, F.54, F.66, L.109, V.113 Chain E: V.748, S.752, N.755, S.756, K.759 Ligands: PC1.3 15 PLIP interactions: 6 interactions with chain D, 7 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: D:L.44, D:L.51, D:F.54, D:F.66, D:L.109, D:V.113, C:T.41, C:V.49, C:V.49, C:V.49, C:L.51, C:F.54, C:F.54, E:V.748 Salt bridges: E:K.759

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 5 residues within 4Å: Chain A: K.623 Chain B: K.25 Chain C: K.25 Chain E: K.727 Ligands: PO4.6 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E, 1 interactions with chain B Salt bridges: A:K.623, C:K.25, E:K.727, B:K.25 PO4.6: 6 residues within 4Å: Chain A: K.623, R.630 Chain B: R.32 Chain D: R.32 Chain E: R.734 Ligands: PO4.5 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 1 interactions with chain B, 1 interactions with chain E Salt bridges: D:R.32, A:K.623, A:R.630, B:R.32 Hydrogen bonds: E:R.734

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guan, Z. et al., The cytoplasmic synthesis and coupled membrane translocation of eukaryotic polyphosphate by signal-activated VTC complex. Nat Commun (2023)

Release Date

2023-02-22

Peptides

Vacuolar transporter chaperone 4: A
Vacuolar transporter chaperone 1: BCD
Vacuolar transporter chaperone 3: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

E
E

Membrane

We predict this structure to be a membrane protein.
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Vacuolar transporter chaperone 4

Vacuolar transporter chaperone 1

Vacuolar transporter chaperone 3